[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years

[Vedat Durmaz]

Hi everybody,


After 7 years I'm trying to do some implicit solvent simulations of
protein-ligand systems again using Gromacs/Amber and running into the
same issue as before:

GB parameter(s) missing or negative for atom type 'N3'
GB parameter(s) missing or negative for atom type 'H'
GB parameter(s) missing or negative for atom type 'CT'
GB parameter(s) missing or negative for atom type 'HP'
GB parameter(s) missing or negative for atom type 'HC'
GB parameter(s) missing or negative for atom type 'H1'
GB parameter(s) missing or negative for atom type 'S'
GB parameter(s) missing or negative for atom type 'C'
GB parameter(s) missing or negative for atom type 'O'
GB parameter(s) missing or negative for atom type 'HA'
GB parameter(s) missing or negative for atom type 'OH'
GB parameter(s) missing or negative for atom type 'HO'
GB parameter(s) missing or negative for atom type 'OS' 

Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 13 atomtypes or they might be negative.

I googled the problem and found a discussion from 2012, which
surprisingly was initialized by myself running into the same issue!  xD

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071102.html

And just as in 2012, I can get my system grompped, although these atom
types listed above are in the force field's gbsa.itp file (apart from
the ether oxygen OS which I added manually as a copy of the carbonyl
atom type "O". Some info:


## My top file:

#include "amber99sb-ildn.ff/forcefield.itp"
#include "ligand.itp"
#include "protein.itp"


## My atom types section at the top of the ligand.itp file:

[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma        
epsilon       Amb
 CT       CT          0.00000  0.00000   A     3.39967e-01   4.57730e-01
; 1.91  0.1094
 HP       HP          0.00000  0.00000   A     1.95998e-01   6.56888e-02
; 1.10  0.0157
 H1       H1          0.00000  0.00000   A     2.47135e-01   6.56888e-02
; 1.39  0.0157
 HC       HC          0.00000  0.00000   A     2.64953e-01   6.56888e-02
; 1.49  0.0157
 S        S           0.00000  0.00000   A     3.56359e-01   1.04600e+00
; 2.00  0.2500
 C        C           0.00000  0.00000   A     3.39967e-01   3.59824e-01
; 1.91  0.0860
 O        O           0.00000  0.00000   A     2.95992e-01   8.78640e-01
; 1.66  0.2100
 N3       N3          0.00000  0.00000   A     3.25000e-01   7.11280e-01
; 1.82  0.1700
 H        H           0.00000  0.00000   A     1.06908e-01   6.56888e-02
; 0.60  0.0157
 N        N           0.00000  0.00000   A     3.25000e-01   7.11280e-01
; 1.82  0.1700
 O2       O2          0.00000  0.00000   A     2.95992e-01   8.78640e-01
; 1.66  0.2100
 CD       CD          0.00000  0.00000   A     3.39967e-01   3.59824e-01
; 1.91  0.0860
 OH       OH          0.00000  0.00000   A     3.06647e-01   8.80314e-01
; 1.72  0.2104
 HO       HO          0.00000  0.00000   A     0.00000e+00   0.00000e+00
; 0.00  0.0000
 CM       CM          0.00000  0.00000   A     3.39967e-01   3.59824e-01
; 1.91  0.0860
 HA       HA          0.00000  0.00000   A     2.59964e-01   6.27600e-02
; 1.46  0.0150
 OS       OS          0.00000  0.00000   A     3.00001e-01   7.11280e-01
; 1.68  0.1700

Did ever anyone find a solution for that issue?

Many thanks!

Vedat